A new class of protein reagents, O-substituted hydroxylamines, is proposed to have a wide applicability in a number of operations related to protein sequencing, selective peptide cleavage, and protein modification. The chemistry of these compounds and related chemistry is incorporated into proposed new methods for carboxyl-terminal residue analysis in proteins; a sequential peptide degradation from the carboxyl terminus; a selective cleavage of polypeptide chains at both tryptophan and carboxylic acid side chains; an analysis for quantitating omega-linkages in Asp and Glu residues in peptides; and protein modification.